Harvest for Steinbauer and Weir 2007 Created 19 Apr 17:19

Stage: completed
Fetched: 19 Apr 17:19
Validated: 19 Apr 17:19
Deltas Created 19 Apr 17:19
Units Normalized: 19 Apr 17:19
Ancestry Built: 19 Apr 17:19
Nodes Matched: 19 Apr 17:19
Names Parsed: 19 Apr 17:19
New Models Stored: 19 Apr 17:19
Indexed: 19 Apr 17:19
Completed: 19 Apr 17:20
Time to Harvest: less than a minute

Harvesting Log

(456 lines)
# Logfile created on 2021-02-03 11:11:47 -0500 by logger.rb/v1.4.2
[START] [2021-02-03 11:11:47] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 11:11:47] Creating resource from OpenData
[START] [2021-02-03 11:11:48] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 11:11:48] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:11:48] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:11:48] Creating resource from OpenData
[INFO] [2021-02-03 11:12:54] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-02-03 11:12:58] ## remove_type: ScientificName
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.114] Removed 0 Scientificnames
[INFO] [2021-02-03 11:12:58] ## remove_type: Vernacular
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.117] Removed 0 Vernaculars
[INFO] [2021-02-03 11:12:58] ## remove_type: Article
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.120] Removed 0 Articles
[INFO] [2021-02-03 11:12:58] ## remove_type: Medium
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.123] Removed 0 Media
[INFO] [2021-02-03 11:12:58] ## remove_type: Trait
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.127] Removed 0 Traits
[INFO] [2021-02-03 11:12:58] ## remove_type: MetaTrait
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.130] Removed 0 Metatraits
[INFO] [2021-02-03 11:12:58] ## remove_type: OccurrenceMetadatum
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.132] Removed 0 Occurrencemetadata
[INFO] [2021-02-03 11:12:58] ## remove_type: Assoc
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.135] Removed 0 Assocs
[INFO] [2021-02-03 11:12:58] ## remove_type: MetaAssoc
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.137] Removed 0 Metaassocs
[INFO] [2021-02-03 11:12:58] ## remove_type: Identifier
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.140] Removed 0 Identifiers
[INFO] [2021-02-03 11:12:58] ## remove_type: Reference
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.142] Removed 0 References
[INFO] [2021-02-03 11:12:58] ## remove_type: Node
[INFO] [2021-02-03 11:12:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:12:58] [11:12:58.175] Removed 0 Nodes
[START] [2021-02-03 11:12:58] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 11:12:58] Creating resource from OpenData
[START] [2021-02-03 11:12:58] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 11:12:58] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:12:58] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:12:58] Creating resource from OpenData
[START] [2021-02-03 11:12:58] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 11:12:58] create_harvest_instance
[STOP] [2021-02-03 11:13:00] create_harvest_instance
[START] [2021-02-03 11:13:00] fetch_files
[STOP] [2021-02-03 11:13:00] fetch_files
[START] [2021-02-03 11:13:00] validate_each_file
[STOP] [2021-02-03 11:13:00] validate_each_file
[START] [2021-02-03 11:13:00] convert_to_csv
[CMD] [2021-02-03 11:13:00] /usr/bin/sort /app/public/converted_csv/steinbauer_weir__nodes_26656.csv > /app/public/converted_csv/steinbauer_weir__nodes_26656.csv_sorted
[CMD] [2021-02-03 11:13:00] /usr/bin/sort /app/public/converted_csv/steinbauer_weir__occurrences_26657.csv > /app/public/converted_csv/steinbauer_weir__occurrences_26657.csv_sorted
[CMD] [2021-02-03 11:13:00] /usr/bin/sort /app/public/converted_csv/steinbauer_weir__measurements_26658.csv > /app/public/converted_csv/steinbauer_weir__measurements_26658.csv_sorted
[STOP] [2021-02-03 11:13:00] convert_to_csv
[START] [2021-02-03 11:13:00] calculate_delta
[CMD] [2021-02-03 11:13:00] echo "0a" > /app/public/diff/steinbauer_weir__nodes_26656.diff
[CMD] [2021-02-03 11:13:00] tail -n +1 /app/public/converted_csv/steinbauer_weir__nodes_26656.csv >> /app/public/diff/steinbauer_weir__nodes_26656.diff
[CMD] [2021-02-03 11:13:00] echo "." >> /app/public/diff/steinbauer_weir__nodes_26656.diff
[CMD] [2021-02-03 11:13:00] echo "0a" > /app/public/diff/steinbauer_weir__occurrences_26657.diff
[CMD] [2021-02-03 11:13:00] tail -n +1 /app/public/converted_csv/steinbauer_weir__occurrences_26657.csv >> /app/public/diff/steinbauer_weir__occurrences_26657.diff
[CMD] [2021-02-03 11:13:00] echo "." >> /app/public/diff/steinbauer_weir__occurrences_26657.diff
[CMD] [2021-02-03 11:13:00] echo "0a" > /app/public/diff/steinbauer_weir__measurements_26658.diff
[CMD] [2021-02-03 11:13:00] tail -n +1 /app/public/converted_csv/steinbauer_weir__measurements_26658.csv >> /app/public/diff/steinbauer_weir__measurements_26658.diff
[CMD] [2021-02-03 11:13:00] echo "." >> /app/public/diff/steinbauer_weir__measurements_26658.diff
[STOP] [2021-02-03 11:13:00] calculate_delta
[START] [2021-02-03 11:13:00] parse_diff_and_store
[INFO] [2021-02-03 11:13:00] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 11:13:00] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 11:13:01] Loading measurements diff file into memory (true lines)...
[INFO] [2021-02-03 11:13:01] Storing 3 ScientificNames
[INFO] [2021-02-03 11:13:01] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 11:13:01] Average Time: 0.0
[INFO] [2021-02-03 11:13:01] Total Time: 1s
[INFO] [2021-02-03 11:13:01] Storing 3 Nodes
[INFO] [2021-02-03 11:13:01] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 11:13:01] Average Time: 0.0
[INFO] [2021-02-03 11:13:01] Total Time: 1s
[INFO] [2021-02-03 11:13:01] Storing 3 Occurrences
[INFO] [2021-02-03 11:13:01] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 11:13:01] Average Time: 0.0
[INFO] [2021-02-03 11:13:01] Total Time: 1s
[INFO] [2021-02-03 11:13:01] Storing 3 OccurrenceMetadata
[INFO] [2021-02-03 11:13:01] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 11:13:01] Average Time: 0.0
[INFO] [2021-02-03 11:13:01] Total Time: 1s
[INFO] [2021-02-03 11:13:01] Storing 6 Traits
[INFO] [2021-02-03 11:13:01] Processing group of 6 in 1 groups of 1000
[INFO] [2021-02-03 11:13:01] Average Time: 0.0
[INFO] [2021-02-03 11:13:01] Total Time: 1s
[INFO] [2021-02-03 11:13:01] Storing 6 MetaTraits
[INFO] [2021-02-03 11:13:01] Processing group of 6 in 1 groups of 1000
[INFO] [2021-02-03 11:13:01] Average Time: 0.0
[INFO] [2021-02-03 11:13:01] Total Time: 1s
[STOP] [2021-02-03 11:13:01] parse_diff_and_store
[START] [2021-02-03 11:13:01] resolve_keys
[INFO] [2021-02-03 11:13:07] Occurrences to nodes (through scientific_names)...
[INFO] [2021-02-03 11:13:07] traits to occurrences...
[INFO] [2021-02-03 11:13:07] traits to nodes (through occurrences)...
[INFO] [2021-02-03 11:13:07] Traits to sex term...
[INFO] [2021-02-03 11:13:07] Traits to lifestage term...
[INFO] [2021-02-03 11:13:07] MetaTraits to traits...
[INFO] [2021-02-03 11:13:07] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-02-03 11:13:07] Assocs to occurrences...
[INFO] [2021-02-03 11:13:07] Assocs to nodes...
[INFO] [2021-02-03 11:13:07] Assoc to sex term...
[INFO] [2021-02-03 11:13:07] Assoc to lifestage term...
[INFO] [2021-02-03 11:13:07] MetaAssoc to assocs...
[STOP] [2021-02-03 11:13:07] resolve_keys
[START] [2021-02-03 11:13:07] hold_for_later_1
[STOP] [2021-02-03 11:13:07] hold_for_later_1
[START] [2021-02-03 11:13:07] hold_for_later_2
[STOP] [2021-02-03 11:13:07] hold_for_later_2
[START] [2021-02-03 11:13:07] resolve_missing_parents
[STOP] [2021-02-03 11:13:07] resolve_missing_parents
[START] [2021-02-03 11:13:07] rebuild_nodes
[START] [2021-02-03 11:13:07] Flattener#flatten
[START] [2021-02-03 11:13:07] Flattener#study_resource
[START] [2021-02-03 11:13:07] Flattener#build_ancestry
[STOP] [2021-02-03 11:13:07] Flattener#build_ancestry
[INFO] [2021-02-03 11:13:07] 3 ancestry keys
[START] [2021-02-03 11:13:07] build_node_ancestors
[INFO] [2021-02-03 11:13:07] old ancestors deleted.
[STOP] [2021-02-03 11:13:07] build_node_ancestors
[WARN] [2021-02-03 11:13:07] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-02-03 11:13:07] Flattener#flatten
[STOP] [2021-02-03 11:13:07] rebuild_nodes
[START] [2021-02-03 11:13:07] resolve_missing_media_owners
[STOP] [2021-02-03 11:13:07] resolve_missing_media_owners
[START] [2021-02-03 11:13:07] sanitize_media_verbatims
[STOP] [2021-02-03 11:13:07] sanitize_media_verbatims
[START] [2021-02-03 11:13:07] queue_downloads
[STOP] [2021-02-03 11:13:07] queue_downloads
[START] [2021-02-03 11:13:07] parse_names
[WARN] [2021-02-03 11:13:07] I see 3 names which still need to be parsed.
[STOP] [2021-02-03 11:13:08] parse_names
[START] [2021-02-03 11:13:08] denormalize_canonical_names_to_nodes
[STOP] [2021-02-03 11:13:08] denormalize_canonical_names_to_nodes
[START] [2021-02-03 11:13:08] match_nodes
[START] [2021-02-03 11:13:08] map_all_nodes_to_pages
[STOP] [2021-02-03 11:13:08] map_all_nodes_to_pages
[INFO] [2021-02-03 11:13:08] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2021-02-03 11:13:08] update_nodes
[STOP] [2021-02-03 11:13:08] update_nodes
[STOP] [2021-02-03 11:13:08] match_nodes
[START] [2021-02-03 11:13:08] reindex_search
[STOP] [2021-02-03 11:13:08] reindex_search
[START] [2021-02-03 11:13:08] normalize_units
[STOP] [2021-02-03 11:13:08] normalize_units
[START] [2021-02-03 11:13:08] calculate_statistics
[2021-02-03 11:13:08] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-02-03 11:13:08] calculate_statistics
[START] [2021-02-03 11:13:08] complete_harvest_instance
[START] [2021-02-03 11:13:08] overall_tsv_creation
[INFO] [2021-02-03 11:13:08] Processing group of 3 in 1 batches of 10000
[INFO] [2021-02-03 11:13:47] 3 Traits (unfiltered)...
[INFO] [2021-02-03 11:14:24] 3 Traits (filtered)...
[INFO] [2021-02-03 11:14:24] 0 Associations (filtered)...
[INFO] [2021-02-03 11:14:24] 9 metadata added.
[INFO] [2021-02-03 11:14:24] 0 metadata added.
[INFO] [2021-02-03 11:14:57] Average Time: 82.97
[INFO] [2021-02-03 11:14:57] Total Time: 1m49s
[STOP] [2021-02-03 11:14:57] overall_tsv_creation
[INFO] [2021-02-03 11:14:57] Done. Check your files:
[INFO] [2021-02-03 11:14:57] (3 lines) /app/public/data/steinbauer_weir_/publish_nodes.tsv
[INFO] [2021-02-03 11:14:57] (3 lines) /app/public/data/steinbauer_weir_/publish_scientific_names.tsv
[INFO] [2021-02-03 11:14:57] (4 lines) /app/public/data/steinbauer_weir_/publish_traits.tsv
[INFO] [2021-02-03 11:14:57] (10 lines) /app/public/data/steinbauer_weir_/publish_metadata.tsv
[STOP] [2021-02-03 11:14:57] complete_harvest_instance
[START] [2021-02-03 11:14:57] completed
[STOP] [2021-02-03 11:14:57] completed
[STOP] [2021-02-03 11:14:57] logged process, took 118.68
[INFO] [2021-04-19 16:54:43] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 17:18:59] ## remove_type: ScientificName
[INFO] [2021-04-19 17:18:59] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 17:18:59] [17:18:59.561] Removed 3 Scientificnames
[INFO] [2021-04-19 17:18:59] ## remove_type: Vernacular
[INFO] [2021-04-19 17:18:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:18:59] [17:18:59.562] Removed 0 Vernaculars
[INFO] [2021-04-19 17:18:59] ## remove_type: Article
[INFO] [2021-04-19 17:18:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:18:59] [17:18:59.563] Removed 0 Articles
[INFO] [2021-04-19 17:18:59] ## remove_type: Medium
[INFO] [2021-04-19 17:18:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:18:59] [17:18:59.565] Removed 0 Media
[INFO] [2021-04-19 17:18:59] ## remove_type: Trait
[INFO] [2021-04-19 17:18:59] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 17:18:59] [17:18:59.567] Removed 6 Traits
[INFO] [2021-04-19 17:18:59] ## remove_type: MetaTrait
[INFO] [2021-04-19 17:18:59] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 17:18:59] [17:18:59.569] Removed 6 Metatraits
[INFO] [2021-04-19 17:18:59] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 17:18:59] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 17:18:59] [17:18:59.571] Removed 3 Occurrencemetadata
[INFO] [2021-04-19 17:18:59] ## remove_type: Assoc
[INFO] [2021-04-19 17:18:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:18:59] [17:18:59.573] Removed 0 Assocs
[INFO] [2021-04-19 17:18:59] ## remove_type: MetaAssoc
[INFO] [2021-04-19 17:18:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:18:59] [17:18:59.574] Removed 0 Metaassocs
[INFO] [2021-04-19 17:18:59] ## remove_type: Identifier
[INFO] [2021-04-19 17:18:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:18:59] [17:18:59.575] Removed 0 Identifiers
[INFO] [2021-04-19 17:18:59] ## remove_type: Reference
[INFO] [2021-04-19 17:18:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:18:59] [17:18:59.576] Removed 0 References
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:18:59] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] Starting batch with ID 87728848...
[INFO] [2021-04-19 17:19:00] ## remove_type: Node
[INFO] [2021-04-19 17:19:00] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 17:19:00] [17:19:00.132] Removed 3 Nodes
[START] [2021-04-19 17:19:00] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:19:00] Creating resource from OpenData
[START] [2021-04-19 17:19:00] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:19:00] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:19:00] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:19:00] Creating resource from OpenData
[START] [2021-04-19 17:19:00] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:19:00] create_harvest_instance
[INFO] [2021-04-19 17:19:00] Created harvest instance #3823
[STOP] [2021-04-19 17:19:00] create_harvest_instance
[START] [2021-04-19 17:19:00] fetch_files
[STOP] [2021-04-19 17:19:00] fetch_files
[START] [2021-04-19 17:19:00] validate_each_file
[INFO] [2021-04-19 17:19:00] Looping over 3 formats...
[INFO] [2021-04-19 17:19:00] ...nodes (/app/public/data/steinbauer_weir_/taxa.txt)
[INFO] [2021-04-19 17:19:00] Valid: /app/public/converted_csv/steinbauer_weir__nodes_3823.csv (3 lines)
[INFO] [2021-04-19 17:19:00] ...occurrences (/app/public/data/steinbauer_weir_/occurrences.txt)
[INFO] [2021-04-19 17:19:00] Valid: /app/public/converted_csv/steinbauer_weir__occurrences_3823.csv (3 lines)
[INFO] [2021-04-19 17:19:00] ...measurements (/app/public/data/steinbauer_weir_/measurementsorfacts.txt)
[INFO] [2021-04-19 17:19:00] Valid: /app/public/converted_csv/steinbauer_weir__measurements_3823.csv (6 lines)
[STOP] [2021-04-19 17:19:00] validate_each_file
[START] [2021-04-19 17:19:00] convert_to_csv
[INFO] [2021-04-19 17:19:00] Looping over 3 formats...
[INFO] [2021-04-19 17:19:00] ...nodes (/app/public/data/steinbauer_weir_/taxa.txt)
[CMD] [2021-04-19 17:19:00] /usr/bin/sort /app/public/converted_csv/steinbauer_weir__nodes_3823.csv > /app/public/converted_csv/steinbauer_weir__nodes_3823.csv_sorted
[INFO] [2021-04-19 17:19:00] Converted: /app/public/converted_csv/steinbauer_weir__nodes_3823.csv (3 lines)
[INFO] [2021-04-19 17:19:00] ...occurrences (/app/public/data/steinbauer_weir_/occurrences.txt)
[CMD] [2021-04-19 17:19:00] /usr/bin/sort /app/public/converted_csv/steinbauer_weir__occurrences_3823.csv > /app/public/converted_csv/steinbauer_weir__occurrences_3823.csv_sorted
[INFO] [2021-04-19 17:19:00] Converted: /app/public/converted_csv/steinbauer_weir__occurrences_3823.csv (3 lines)
[INFO] [2021-04-19 17:19:00] ...measurements (/app/public/data/steinbauer_weir_/measurementsorfacts.txt)
[CMD] [2021-04-19 17:19:00] /usr/bin/sort /app/public/converted_csv/steinbauer_weir__measurements_3823.csv > /app/public/converted_csv/steinbauer_weir__measurements_3823.csv_sorted
[INFO] [2021-04-19 17:19:00] Converted: /app/public/converted_csv/steinbauer_weir__measurements_3823.csv (6 lines)
[STOP] [2021-04-19 17:19:00] convert_to_csv
[START] [2021-04-19 17:19:00] calculate_delta
[INFO] [2021-04-19 17:19:00] Looping over 3 formats...
[INFO] [2021-04-19 17:19:00] ...nodes (/app/public/data/steinbauer_weir_/taxa.txt)
[CMD] [2021-04-19 17:19:00] echo "0a" > /app/public/diff/steinbauer_weir__nodes_3823.diff
[CMD] [2021-04-19 17:19:00] tail -n +1 /app/public/converted_csv/steinbauer_weir__nodes_3823.csv >> /app/public/diff/steinbauer_weir__nodes_3823.diff
[CMD] [2021-04-19 17:19:00] echo "." >> /app/public/diff/steinbauer_weir__nodes_3823.diff
[INFO] [2021-04-19 17:19:00] Created diff: /app/public/diff/steinbauer_weir__nodes_3823.diff (5 lines)
[INFO] [2021-04-19 17:19:00] ...occurrences (/app/public/data/steinbauer_weir_/occurrences.txt)
[CMD] [2021-04-19 17:19:00] echo "0a" > /app/public/diff/steinbauer_weir__occurrences_3823.diff
[CMD] [2021-04-19 17:19:00] tail -n +1 /app/public/converted_csv/steinbauer_weir__occurrences_3823.csv >> /app/public/diff/steinbauer_weir__occurrences_3823.diff
[CMD] [2021-04-19 17:19:00] echo "." >> /app/public/diff/steinbauer_weir__occurrences_3823.diff
[INFO] [2021-04-19 17:19:00] Created diff: /app/public/diff/steinbauer_weir__occurrences_3823.diff (5 lines)
[INFO] [2021-04-19 17:19:00] ...measurements (/app/public/data/steinbauer_weir_/measurementsorfacts.txt)
[CMD] [2021-04-19 17:19:00] echo "0a" > /app/public/diff/steinbauer_weir__measurements_3823.diff
[CMD] [2021-04-19 17:19:00] tail -n +1 /app/public/converted_csv/steinbauer_weir__measurements_3823.csv >> /app/public/diff/steinbauer_weir__measurements_3823.diff
[CMD] [2021-04-19 17:19:00] echo "." >> /app/public/diff/steinbauer_weir__measurements_3823.diff
[INFO] [2021-04-19 17:19:00] Created diff: /app/public/diff/steinbauer_weir__measurements_3823.diff (8 lines)
[STOP] [2021-04-19 17:19:00] calculate_delta
[START] [2021-04-19 17:19:00] parse_diff_and_store
[INFO] [2021-04-19 17:19:00] Handling diff: /app/public/diff/steinbauer_weir__nodes_3823.diff (5 lines)
[INFO] [2021-04-19 17:19:00] Loading nodes diff file into memory (5 /app/public/diff/steinbauer_weir__nodes_3823.diff lines)...
[INFO] [2021-04-19 17:19:00] Handling diff: /app/public/diff/steinbauer_weir__occurrences_3823.diff (5 lines)
[INFO] [2021-04-19 17:19:00] Loading occurrences diff file into memory (5 /app/public/diff/steinbauer_weir__occurrences_3823.diff lines)...
[INFO] [2021-04-19 17:19:00] Handling diff: /app/public/diff/steinbauer_weir__measurements_3823.diff (8 lines)
[INFO] [2021-04-19 17:19:00] Loading measurements diff file into memory (8 /app/public/diff/steinbauer_weir__measurements_3823.diff lines)...
[INFO] [2021-04-19 17:19:00] Storing 3 ScientificNames
[INFO] [2021-04-19 17:19:00] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:19:00] Average Time: 0.0
[INFO] [2021-04-19 17:19:00] Total Time: 1s
[INFO] [2021-04-19 17:19:00] Storing 3 Nodes
[INFO] [2021-04-19 17:19:00] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:19:00] Average Time: 0.0
[INFO] [2021-04-19 17:19:00] Total Time: 1s
[INFO] [2021-04-19 17:19:00] Storing 3 Occurrences
[INFO] [2021-04-19 17:19:00] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:19:00] Average Time: 0.0
[INFO] [2021-04-19 17:19:00] Total Time: 1s
[INFO] [2021-04-19 17:19:00] Storing 3 OccurrenceMetadata
[INFO] [2021-04-19 17:19:00] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:19:00] Average Time: 0.0
[INFO] [2021-04-19 17:19:00] Total Time: 1s
[INFO] [2021-04-19 17:19:00] Storing 6 Traits
[INFO] [2021-04-19 17:19:00] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 17:19:00] Average Time: 0.0
[INFO] [2021-04-19 17:19:00] Total Time: 1s
[INFO] [2021-04-19 17:19:00] Storing 6 MetaTraits
[INFO] [2021-04-19 17:19:00] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 17:19:00] Average Time: 0.0
[INFO] [2021-04-19 17:19:00] Total Time: 1s
[STOP] [2021-04-19 17:19:00] parse_diff_and_store
[START] [2021-04-19 17:19:00] resolve_keys
[INFO] [2021-04-19 17:19:06] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 17:19:06] traits to occurrences...
[INFO] [2021-04-19 17:19:06] traits to nodes (through occurrences)...
[INFO] [2021-04-19 17:19:06] Traits to sex term...
[INFO] [2021-04-19 17:19:06] Traits to lifestage term...
[INFO] [2021-04-19 17:19:06] MetaTraits to traits...
[INFO] [2021-04-19 17:19:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 17:19:06] Assocs to occurrences...
[INFO] [2021-04-19 17:19:06] Assocs to nodes...
[INFO] [2021-04-19 17:19:06] Assoc to sex term...
[INFO] [2021-04-19 17:19:06] Assoc to lifestage term...
[INFO] [2021-04-19 17:19:06] MetaAssoc to assocs...
[STOP] [2021-04-19 17:19:06] resolve_keys
[START] [2021-04-19 17:19:06] hold_for_later_1
[STOP] [2021-04-19 17:19:06] hold_for_later_1
[START] [2021-04-19 17:19:06] hold_for_later_2
[STOP] [2021-04-19 17:19:06] hold_for_later_2
[START] [2021-04-19 17:19:06] resolve_missing_parents
[STOP] [2021-04-19 17:19:06] resolve_missing_parents
[START] [2021-04-19 17:19:06] rebuild_nodes
[START] [2021-04-19 17:19:06] Flattener#flatten
[START] [2021-04-19 17:19:06] Flattener#study_resource
[START] [2021-04-19 17:19:06] Flattener#build_ancestry
[STOP] [2021-04-19 17:19:06] Flattener#build_ancestry
[INFO] [2021-04-19 17:19:06] 3 ancestry keys
[START] [2021-04-19 17:19:06] build_node_ancestors
[INFO] [2021-04-19 17:19:06] old ancestors deleted.
[STOP] [2021-04-19 17:19:06] build_node_ancestors
[WARN] [2021-04-19 17:19:06] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 17:19:06] Flattener#flatten
[STOP] [2021-04-19 17:19:06] rebuild_nodes
[START] [2021-04-19 17:19:06] resolve_missing_media_owners
[STOP] [2021-04-19 17:19:06] resolve_missing_media_owners
[START] [2021-04-19 17:19:06] sanitize_media_verbatims
[STOP] [2021-04-19 17:19:06] sanitize_media_verbatims
[START] [2021-04-19 17:19:06] queue_downloads
[STOP] [2021-04-19 17:19:06] queue_downloads
[START] [2021-04-19 17:19:06] parse_names
[WARN] [2021-04-19 17:19:06] I see 3 names which still need to be parsed.
[STOP] [2021-04-19 17:19:07] parse_names
[START] [2021-04-19 17:19:07] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 17:19:07] denormalize_canonical_names_to_nodes
[START] [2021-04-19 17:19:08] match_nodes
[START] [2021-04-19 17:19:08] map_all_nodes_to_pages
[STOP] [2021-04-19 17:19:08] map_all_nodes_to_pages
[INFO] [2021-04-19 17:19:08] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2021-04-19 17:19:08] update_nodes
[STOP] [2021-04-19 17:19:08] update_nodes
[STOP] [2021-04-19 17:19:08] match_nodes
[START] [2021-04-19 17:19:08] reindex_search
[STOP] [2021-04-19 17:19:08] reindex_search
[START] [2021-04-19 17:19:08] normalize_units
[STOP] [2021-04-19 17:19:08] normalize_units
[START] [2021-04-19 17:19:08] calculate_statistics
[2021-04-19 17:19:08] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 17:19:08] calculate_statistics
[START] [2021-04-19 17:19:08] complete_harvest_instance
[START] [2021-04-19 17:19:08] overall_tsv_creation
[INFO] [2021-04-19 17:19:08] Processing group of 3 in 1 batches of 10000
[INFO] [2021-04-19 17:19:43] 3 Traits (unfiltered)...
[INFO] [2021-04-19 17:20:17] 3 Traits (filtered)...
[INFO] [2021-04-19 17:20:17] 0 Associations (filtered)...
[INFO] [2021-04-19 17:20:17] 3 metadata added.
[INFO] [2021-04-19 17:20:17] 0 metadata added.
[INFO] [2021-04-19 17:20:43] Average Time: 71.7
[INFO] [2021-04-19 17:20:43] Total Time: 1m36s
[STOP] [2021-04-19 17:20:43] overall_tsv_creation
[INFO] [2021-04-19 17:20:43] Done. Check your files:
[INFO] [2021-04-19 17:20:43] (3 lines) /app/public/data/steinbauer_weir_/publish_nodes.tsv
[INFO] [2021-04-19 17:20:43] (3 lines) /app/public/data/steinbauer_weir_/publish_scientific_names.tsv
[INFO] [2021-04-19 17:20:43] (4 lines) /app/public/data/steinbauer_weir_/publish_traits.tsv
[INFO] [2021-04-19 17:20:43] (4 lines) /app/public/data/steinbauer_weir_/publish_metadata.tsv
[STOP] [2021-04-19 17:20:43] complete_harvest_instance
[START] [2021-04-19 17:20:43] completed
[STOP] [2021-04-19 17:20:43] completed
[STOP] [2021-04-19 17:20:43] logged process, took 102.99

Latest Process